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Commit 2e516028 authored by Jérôme Euzenat's avatar Jérôme Euzenat
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- OWL API 1 is not the default anymore

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lib/owlapi1/api.jar deleted 100644 → 0
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src/fr/inrialpes/exmo/align/onto/owlapi10/OWLAPIAnnotIt.java deleted 100644 → 0
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package fr.inrialpes.exmo.align.onto.owlapi10;
import java.util.Iterator;
import java.util.NoSuchElementException;
import org.semanticweb.owl.model.OWLAnnotationInstance;
import org.semanticweb.owl.model.OWLDataValue;
import org.semanticweb.owl.model.OWLEntity;
import org.semanticweb.owl.model.OWLException;
import org.semanticweb.owl.model.OWLOntology;
/**
* An iterator over annotations of an OWLEntity. This class permits to avoid the instantiation of HashSet for
* each call of a getAnnotation method.
* @author JD
*
*/
public class OWLAPIAnnotIt implements Iterator<String> {
/*private OWLOntology o;
private OWLEntity e;*/
private String lang;
private String typeAnnot;
private Iterator it;
private String currentElem=null;
public OWLAPIAnnotIt(OWLOntology o, OWLEntity e , String lang , String typeAnnot) throws OWLException {
/*this.o=o; this.e=e; */ this.lang=lang; this.typeAnnot=typeAnnot;
it = e.getAnnotations(o).iterator();
}
public boolean hasNext() {
try {
setNext();
return currentElem != null;
}
catch (NoSuchElementException e) {
return false;
}
}
public String next() {
setNext();
String returnVal = currentElem;
currentElem=null;
return returnVal;
}
private void setNext() throws NoSuchElementException {
while (currentElem==null) {
OWLAnnotationInstance annot = (OWLAnnotationInstance) it.next();
try {
String annotUri = annot.getProperty().getURI().toString();
if (annotUri.equals(typeAnnot) || typeAnnot==null) {
if ( annot.getContent() instanceof OWLDataValue &&
( lang==null || ((OWLDataValue) annot.getContent()).getLang().equals(lang)) ) {
currentElem = ((OWLDataValue) annot.getContent()).getValue().toString();
}
}
} catch (OWLException e) {
e.printStackTrace();
currentElem=null;
}
}
}
public void remove() {
throw new UnsupportedOperationException();
}
}
src/fr/inrialpes/exmo/align/onto/owlapi10/OWLAPIOntology.java deleted 100644 → 0
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/*
* $Id$
*
* Copyright (C) INRIA, 2007-2008
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as published by
* the Free Software Foundation; either version 2.1 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
/*
* This should be turned into an HeavyLoadedOntology.
* Some primitives are already avalible below
*
* The point is that these primitives may concern:
* - Named entities / All entities
* - Asserted information / Deduced information
* - Inherited information... ()
* In fact the OWL API does only provide asserted.
*
* This is not very well implemented: the OWL API mandates to implement this as visitors...
*/
package fr.inrialpes.exmo.align.onto.owlapi10;
import java.net.URI;
import java.util.AbstractSet;
import java.util.Iterator;
import java.util.Set;
import java.util.HashSet;
import org.semanticweb.owl.align.AlignmentException;
import fr.inrialpes.exmo.align.onto.OntologyFactory;
import fr.inrialpes.exmo.align.onto.HeavyLoadedOntology;
import fr.inrialpes.exmo.align.onto.BasicOntology;
import org.semanticweb.owl.io.vocabulary.RDFSVocabularyAdapter;
import org.semanticweb.owl.model.OWLAnnotationInstance;
import org.semanticweb.owl.model.OWLDataType;
import org.semanticweb.owl.model.OWLDataValue;
import org.semanticweb.owl.model.OWLOntology;
import org.semanticweb.owl.model.OWLProperty;
import org.semanticweb.owl.model.OWLClass;
import org.semanticweb.owl.model.OWLObjectProperty;
import org.semanticweb.owl.model.OWLDataProperty;
import org.semanticweb.owl.model.OWLIndividual;
import org.semanticweb.owl.model.OWLEntity;
import org.semanticweb.owl.model.OWLRestriction;
import org.semanticweb.owl.model.OWLDescription;
import org.semanticweb.owl.model.OWLNaryBooleanDescription;
import org.semanticweb.owl.model.OWLCardinalityRestriction;
import org.semanticweb.owl.model.OWLDataAllRestriction;
import org.semanticweb.owl.model.OWLObjectAllRestriction;
import org.semanticweb.owl.model.OWLException;
import org.semanticweb.owl.model.helper.OWLEntityCollector;
/**
* Store the information regarding ontologies in a specific structure
* Acts as an interface with regard to an ontology APY
*/
public class OWLAPIOntology extends BasicOntology<OWLOntology> implements HeavyLoadedOntology<OWLOntology> {
/* For caching sizes */
private int nbentities = -1;
private int nbclasses = -1;
private int nbproperties = -1;
private int nbobjectproperties = -1;
private int nbdataproperties = -1;
private int nbindividuals = -1;
public OWLAPIOntology() {
setFormalism( "OWL1.0" );
try {
setFormURI( new URI("http://www.w3.org/2002/07/owl#") );
} catch (Exception e) {}; // does not happen
};
// -----------------------------------------------------------------
// Ontology interface [//DONE]
public OWLOntology getOntology() { return onto; }
public void setOntology( OWLOntology o ) { this.onto = o; }
// -----------------------------------------------------------------
// LoadedOntology interface [//DONE]
public Object getEntity( URI uri ) throws AlignmentException {
try {
OWLEntity result = ((OWLOntology)onto).getClass( uri );
if ( result == null ) result = ((OWLOntology)onto).getDataProperty( uri );
if ( result == null ) result = ((OWLOntology)onto).getObjectProperty( uri );
if ( result == null ) result = ((OWLOntology)onto).getIndividual( uri );
return result;
} catch (OWLException ex) {
throw new AlignmentException( "Cannot dereference URI : "+uri );
}
}
public URI getEntityURI( Object o ) throws AlignmentException {
try {
return ((OWLEntity)o).getURI();
} catch (OWLException oex) {
throw new AlignmentException( "Cannot get URI ", oex );
}
}
public String getEntityName( Object o ) throws AlignmentException {
try {
// Try to get labels first...
URI u = ((OWLEntity)o).getURI();
if ( u != null ) return u.getFragment();
else return "";
} catch (OWLException oex) {
return null;
}
};
public Set<String> getEntityNames( Object o , String lang ) throws AlignmentException {
try {
OWLEntity e = ((OWLEntity) o);
return getAnnotations(e,lang,RDFSVocabularyAdapter.INSTANCE.getLabel());
} catch (OWLException oex) {
return null;
}
}
public Set<String> getEntityNames( Object o ) throws AlignmentException {
try {
OWLEntity e = ((OWLEntity) o);
return getAnnotations(e,null,RDFSVocabularyAdapter.INSTANCE.getLabel());
} catch (OWLException oex) {
return null;
}
};
public Set<String> getEntityComments( Object o , String lang ) throws AlignmentException {
try {
OWLEntity e = ((OWLEntity) o);
return getAnnotations(e,lang,RDFSVocabularyAdapter.INSTANCE.getComment());
} catch (OWLException oex) {
return null;
}
};
public Set<String> getEntityComments( Object o ) throws AlignmentException {
try {
OWLEntity e = ((OWLEntity) o);
return getAnnotations(e,null,RDFSVocabularyAdapter.INSTANCE.getComment());
} catch (OWLException oex) {
return null;
}
};
protected Set<String> getAnnotations(final OWLEntity e , final String lang , final String typeAnnot ) throws OWLException {
final OWLOntology o = this.onto;
return new AbstractSet<String>() {
int size=-1;
public Iterator<String> iterator() {
try {
return new OWLAPIAnnotIt(o,e,lang,typeAnnot);
} catch (OWLException e) {
e.printStackTrace();
return null;
}
}
public int size() {
if (size==-1) {
for (String s : this) {
size++;
}
size++;
}
return size;
}
};
// OLD IMPLEMENTATION
/*Set<String> annots = new HashSet<String>();
for (Object objAnnot : e.getAnnotations(onto)) {
OWLAnnotationInstance annot = (OWLAnnotationInstance) objAnnot;
String annotUri = annot.getProperty().getURI().toString();
if (annotUri.equals(typeAnnot) || typeAnnot==null) {
if ( annot.getContent() instanceof OWLDataValue &&
( lang==null || ((OWLDataValue) annot.getContent()).getLang().equals(lang)) ) {
annots.add(((OWLDataValue) annot.getContent()).getValue().toString());
}
}
}
return annots;*/
}
public Set<String> getEntityAnnotations( Object o ) throws AlignmentException {
try {
return getAnnotations(((OWLEntity) o),null,null);
} catch (OWLException oex) {
return null;
}
};
public boolean isEntity( Object o ){
return ( o instanceof OWLEntity );
};
public boolean isClass( Object o ){
return ( o instanceof OWLClass );
};
public boolean isProperty( Object o ){
return ( o instanceof OWLProperty );
};
public boolean isDataProperty( Object o ){
return ( o instanceof OWLDataProperty );
};
public boolean isObjectProperty( Object o ){
return ( o instanceof OWLObjectProperty );
};
public boolean isIndividual( Object o ){
return ( o instanceof OWLIndividual );
};
// ***JE:
// We should solve this issue, is it better to go this way or tu use the OWL API?
// JD: allows to retrieve some specific entities by giving their class
// This is not part of the interface...
protected Set<?> getEntities(Class<? extends OWLEntity> c) throws OWLException{
OWLEntityCollector ec = new OWLEntityCollector();
onto.accept(ec);
Set<Object> entities = new HashSet<Object>();
for (Object obj : ec.entities()) {
// JD: OWLEntitytCollector seems to return anonymous entities :&& ((OWLEntity)obj).getURI()!=null
if (c.isInstance(obj) && ((OWLEntity) obj).getURI()!=null) { // &&((OWLEntity) obj).getURI().toString().startsWith(onto.getURI().toString()) ){
entities.add(obj);
}
}
return entities;
}
// Here it shoud be better to report exception
// JE: Onto this does not work at all, of course...!!!!
public Set<?> getEntities() {
try {
return getEntities(OWLEntity.class);
} catch (OWLException ex) {
return null;
}
}
public Set<?> getClasses() {
try {
return ((OWLOntology)onto).getClasses(); // [W:unchecked]
//return getEntities(OWLClass.class);
} catch (OWLException ex) {
return null;
}
}
public Set<?> getProperties() {
try {
//return ((OWLOntology)onto).getProperties(); // [W:unchecked]
return getEntities(OWLProperty.class);
} catch (OWLException ex) {
return null;
}
}
public Set<?> getDataProperties() {
try {
// This first method returns also Properties not defined in the Onto
// i.e. properties having an namespace different from the ontology uri
return ((OWLOntology)onto).getDataProperties(); // [W:unchecked]
//return getEntities(OWLDataProperty.class);
} catch (OWLException ex) {
return null;
}
}
public Set<?> getObjectProperties() {
try {
// [Warning:unchecked] due to OWL API not serving generic types
// This first method returns also Properties not defined in the Onto
// i.e. properties having an namespace different from the ontology uri
return ((OWLOntology)onto).getObjectProperties(); // [W:unchecked]
// This method works better (??)
//return getEntities(OWLObjectProperty.class);
} catch (OWLException ex) {
return null;
}
}
public Set<?> getIndividuals() {
try {
return ((OWLOntology)onto).getIndividuals(); // [W:unchecked]
//return getEntities(OWLIndividual.class);
} catch (OWLException ex) {
return null;
}
}
public int nbEntities() {
if ( nbentities != -1 ) return nbentities;
nbentities = nbClasses()+nbProperties()+nbIndividuals();
return nbentities;
}
public int nbClasses() {
if ( nbclasses != -1 ) return nbclasses;
try {
nbclasses = ((OWLOntology)onto).getClasses().size();
return nbclasses;
} catch (OWLException oex) {
return 0;
}
}
public int nbProperties() {
if ( nbproperties != -1 ) return nbproperties;
nbproperties = nbObjectProperties()+nbDataProperties();
return nbproperties;
}
public int nbObjectProperties() {
if ( nbobjectproperties != -1 ) return nbobjectproperties;
try {
nbobjectproperties = ((OWLOntology)onto).getObjectProperties().size();
return nbobjectproperties;
} catch (OWLException oex) {
return 0;
}
}
public int nbDataProperties() {
if ( nbdataproperties != -1 ) return nbdataproperties;
try {
nbdataproperties = ((OWLOntology)onto).getDataProperties().size();
return nbdataproperties;
} catch (OWLException oex) {
return 0;
}
}
public int nbIndividuals() {
if ( nbindividuals != -1 ) return nbindividuals;
try {
nbindividuals = ((OWLOntology)onto).getIndividuals().size();
return nbindividuals;
} catch (OWLException oex) {
return 0;
}
}
public void unload() {
try {
((OWLOntology)onto).getOWLConnection().notifyOntologyDeleted( ((OWLOntology)onto) );
} catch (OWLException ex) { System.err.println(ex); };
}
// -----------------------------------------------------------------
// HeavyLoadedOntology interface [//TOCHECK]
// [//TODO]
public boolean getCapabilities( int Direct, int Asserted, int Named ){
return true;
}
// Pretty inefficient but nothing seems to be stored
public Set<Object> getSubClasses( Object cl, int local, int asserted, int named ){
Set<Object> sbcl = new HashSet<Object>();
for( Object c : getClasses() ) {
if ( getSuperClasses( (OWLClass)c, local, asserted, named ).contains( cl ) ) sbcl.add( c );
}
return sbcl;
}
public Set<Object> getSuperClasses( Object cl, int local, int asserted, int named ){
Set<Object> spcl = new HashSet<Object>();
if ( asserted == OntologyFactory.ASSERTED ){
try {
for( Object rest : ((OWLClass)cl).getSuperClasses( getOntology() ) ){
if (rest instanceof OWLClass) spcl.add( rest );
}
} catch (OWLException ex) {
}
} else {
try {
// JE: I do not feel that this is really correct
Set<Object> sup = new HashSet<Object>();
for( Object rest : ((OWLClass)cl).getSuperClasses( getOntology() ) ){
if (rest instanceof OWLClass) {
spcl.add( rest );
sup.add( rest );
}
}
} catch (OWLException ex) {
};
}
return spcl;
}
/*
* In the OWL API, there is no properties: there are SuperClasses which are restrictions
*/
public Set<Object> getProperties( Object cl, int local, int asserted, int named ){
Set<Object> prop = new HashSet<Object>();
if ( asserted == OntologyFactory.ASSERTED && local == OntologyFactory.LOCAL ) {
try {
for ( Object ent : ((OWLClass)cl).getSuperClasses( getOntology() ) ){
if ( ent instanceof OWLRestriction )
prop.add( ((OWLRestriction)ent).getProperty() );
}
} catch (OWLException e) { e.printStackTrace(); }
} else {
prop = getInheritedProperties( (OWLClass)cl );
}
return prop;
}
// Not very efficient: 2n instead of n
public Set<Object> getDataProperties( Object c, int local, int asserted, int named ){
Set<Object> props = new HashSet<Object>();
for ( Object p : getProperties( c, local, asserted, named ) ){
if ( p instanceof OWLDataProperty ) props.add( p );
}
return props;
}
// Not very efficient: 2n instead of n
public Set<Object> getObjectProperties( Object c, int local, int asserted, int named ){
Set<Object> props = new HashSet<Object>();
for ( Object p : getProperties( c, local, asserted, named ) ){
if ( p instanceof OWLObjectProperty ) props.add( p );
}
return props;
}
// Pretty inefficient but nothing seems to be stored
public Set<Object> getInstances( Object cl, int local, int asserted, int named ){
Set<Object> sbcl = new HashSet<Object>();
try {
for( Object i : getIndividuals() ) {
//if ( getClasses( (OWLIndividual)i, local, asserted, named ).contains( cl ) ) sbcl.add( i );
if ( ((OWLIndividual)i).getTypes( getOntology() ).contains( cl ) ) sbcl.add( i );
}
} catch (OWLException ex) {};
return sbcl;
}
// Pretty inefficient but nothing seems to be stored
public Set<Object> getSubProperties( Object pr, int local, int asserted, int named ){
Set<Object> sbpr = new HashSet<Object>();
for( Object p : getProperties() ) {
if ( getSuperProperties( (OWLProperty)p, local, asserted, named ).contains( pr ) ) sbpr.add( p );
}
return sbpr;
}
public Set<Object> getSuperProperties( Object pr, int local, int asserted, int named ){
Set<Object> supers = new HashSet<Object>();
if ( asserted == OntologyFactory.ASSERTED ){
try {
for( Object rest : ((OWLProperty)pr).getSuperProperties( getOntology() ) ){
if (rest instanceof OWLProperty) supers.add( rest );
}
} catch (OWLException ex) {
}
} else {
try {
Set<Object> sup = new HashSet<Object>();
for( Object rest : ((OWLProperty)pr).getSuperProperties( getOntology() ) ){
if (rest instanceof OWLProperty) {
sup.add( rest );
supers.add( rest );
}
}
} catch (OWLException ex) {
};
}
return supers;
}
public Set<Object> getRange( Object p, int asserted ){
Set resultSet = new HashSet();
try {
for ( Object ent : ((OWLProperty)p).getRanges( getOntology() ) ){
// Not correct
// Could be something else than class
if ( ent instanceof OWLClass || ent instanceof OWLDataType ) {
resultSet.add( ent );
}
}
} catch (OWLException ex) {};
return resultSet;
}
public Set<Object> getDomain( Object p, int asserted ){
Set resultSet = new HashSet();
try {
for ( Object ent : ((OWLProperty)p).getDomains( getOntology() ) ){
// Not correct
// Could be something else than class
if ( ent instanceof OWLClass ) {
resultSet.add( ent );
}
}
} catch (OWLException ex) {};
return resultSet;
}
public Set<Object> getClasses( Object i, int local, int asserted, int named ){
Set<Object> supers = null;
try {
supers = ((OWLIndividual)i).getTypes( getOntology() );
} catch (OWLException ex) {};
if ( local == OntologyFactory.LOCAL ) {
return supers;
} else {
// inherits the superclasses (unless we have to reduce them...)
return supers;
}
}
// JE: note this may be wrong if p is a property
public Set<Object> getCardinalityRestrictions( Object p ){//JFDK
Set<Object> spcl = new HashSet<Object>();
try {
Set<Object> sup = ((OWLClass)p).getSuperClasses( getOntology() );
for( Object rest : sup ){
// This should be filtered
if (rest instanceof OWLCardinalityRestriction) spcl.add( rest );
}
} catch (OWLException ex) {
};
return spcl;
}
/*
* Inherits all properties of a class
*/
private Set<Object> getInheritedProperties( OWLClass cl ) {
Set resultSet = new HashSet();
try { getProperties( cl, resultSet ); }
catch (OWLException ex) {};
return resultSet;
}
/* This traverse properties */
public void getProperties( OWLDescription desc, Set<Object> list) throws OWLException {
if ( desc instanceof OWLRestriction ){
//getProperties( (OWLRestriction)desc, list );
list.add( ((OWLRestriction)desc).getProperty() );
} else if ( desc instanceof OWLClass ) {
getProperties( (OWLClass)desc, list );
} else if ( desc instanceof OWLNaryBooleanDescription ) {
for ( Object d : ((OWLNaryBooleanDescription)desc).getOperands() ){
getProperties( (OWLDescription)d, list );
}
//getProperties( (OWLNaryBooleanDescription)desc, list );
}
}
public void getProperties( OWLRestriction rest, Set<Object> list) throws OWLException {
list.add( (Object)rest.getProperty() );
}
public void getProperties( OWLNaryBooleanDescription d, Set<Object> list) throws OWLException {
for ( Iterator it = d.getOperands().iterator(); it.hasNext() ;){
getProperties( (OWLDescription)it.next(), list );
}
}
public void getProperties( OWLClass cl, Set<Object> list) throws OWLException {
for ( Object desc : cl.getSuperClasses( getOntology() ) ){
getProperties( (OWLDescription)desc, list );
}
// JE: I suspect that this can be a cause for looping!!
for ( Object desc : cl.getEquivalentClasses( getOntology() ) ){
getProperties( (OWLDescription)desc, list );
}
}
}
src/fr/inrialpes/exmo/align/onto/owlapi10/OWLAPIOntologyFactory.java deleted 100644 → 0
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/*
* $Id$
*
* Copyright (C) INRIA, 2008
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as published by
* the Free Software Foundation; either version 2.1 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
package fr.inrialpes.exmo.align.onto.owlapi10;
import java.net.URI;
import java.net.URISyntaxException;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
import org.apache.log4j.Logger;
import org.apache.log4j.Level;
import org.semanticweb.owl.align.AlignmentException;
import fr.inrialpes.exmo.align.onto.OntologyCache;
import fr.inrialpes.exmo.align.onto.OntologyFactory;
import fr.inrialpes.exmo.align.onto.Ontology;
import fr.inrialpes.exmo.align.onto.LoadedOntology;
import org.semanticweb.owl.model.OWLException;
import org.semanticweb.owl.model.OWLOntology;
import org.semanticweb.owl.util.OWLConnection;
import org.semanticweb.owl.util.OWLManager;
public class OWLAPIOntologyFactory extends OntologyFactory {
private static URI formalismUri = null;
private static String formalismId = "OWL1.0";
private static OntologyCache<OWLAPIOntology> cache = null;
public OWLAPIOntologyFactory() {
cache = new OntologyCache<OWLAPIOntology>();
try {
formalismUri = new URI("http://www.w3.org/2002/07/owl#");
} catch (URISyntaxException ex) { ex.printStackTrace(); } // should not happen
};
public void clearCache() {
cache.clear();
}
public OWLAPIOntology newOntology( Object ontology ) throws AlignmentException {
if ( ontology instanceof OWLOntology ) {
OWLAPIOntology onto = new OWLAPIOntology();
onto.setFormalism( formalismId );
onto.setFormURI( formalismUri );
onto.setOntology( (OWLOntology)ontology );
//onto.setFile( uri );// unknown
try {
onto.setURI( ((OWLOntology)ontology).getLogicalURI() );
} catch (OWLException e) {
// Better put in the AlignmentException of loaded
e.printStackTrace();
}
//cache.recordOntology( uri, onto );
return onto;
} else {
throw new AlignmentException( "Argument is not an OWLOntology: "+ontology );
}
}
public OWLAPIOntology loadOntology( URI uri ) throws AlignmentException {
OWLAPIOntology onto = null;
onto = cache.getOntologyFromURI( uri );
if ( onto != null ) return onto;
onto = cache.getOntology( uri );
if ( onto != null ) return onto;
OWLConnection connection = null;
Map<Object,Object> parameters = new HashMap<Object, Object>();
parameters.put(OWLManager.OWL_CONNECTION,
"org.semanticweb.owl.impl.model.OWLConnectionImpl");
try {
connection = OWLManager.getOWLConnection(parameters);
Level lev = Logger.getLogger("org.semanticweb.owl").getLevel();
Logger.getLogger("org.semanticweb.owl").setLevel(Level.ERROR);
OWLOntology ontology = connection.loadOntologyPhysical(uri);
Logger.getLogger("org.semanticweb.owl").setLevel(lev);
onto = new OWLAPIOntology();
// It may be possible to fill this as final in OWLAPIOntology...
onto.setFormalism( formalismId );
onto.setFormURI( formalismUri );
onto.setOntology( ontology );
onto.setFile( uri );
try {
onto.setURI( ontology.getLogicalURI() );
} catch (OWLException e) {
// Better put in the AlignmentException of loaded
e.printStackTrace();
}
cache.recordOntology( uri, onto );
return onto;
} catch (OWLException e) {
throw new AlignmentException("Cannot load "+uri, e );
}
}
}
test/src/OWLAPIAlignmentTest.java deleted 100644 → 0
+ 0
− 162
View file @ b7e92dc0
/*
* $Id$
*
* Copyright (C) INRIA, 2008
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as published by
* the Free Software Foundation; either version 2.1 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
//package test.com.acme.dona.dep;
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertNotNull;
import static org.testng.Assert.assertNull;
import static org.testng.Assert.assertTrue;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Configuration;
import org.testng.annotations.Test;
//import org.testng.annotations.*;
import org.semanticweb.owl.model.OWLOntology;
import org.semanticweb.owl.model.OWLEntity;
import org.semanticweb.owl.align.AlignmentVisitor;
import org.semanticweb.owl.align.Cell;
import fr.inrialpes.exmo.align.impl.OWLAPIAlignment;
import fr.inrialpes.exmo.align.impl.OWLAPICell;
import fr.inrialpes.exmo.align.impl.rel.EquivRelation;
import fr.inrialpes.exmo.align.impl.URIAlignment;
import fr.inrialpes.exmo.align.impl.Annotations;
import fr.inrialpes.exmo.align.impl.renderer.RDFRendererVisitor;
import fr.inrialpes.exmo.align.onto.LoadedOntology;
import fr.inrialpes.exmo.align.onto.Ontology;
import fr.inrialpes.exmo.align.parser.AlignmentParser;
import java.io.ByteArrayOutputStream;
import java.io.PrintWriter;
import java.io.BufferedWriter;
import java.io.OutputStreamWriter;
import java.io.FileOutputStream;
import java.net.URI;
import java.util.Set;
public class OWLAPIAlignmentTest {
private String localURIPrefix = "file://" + System.getProperty("user.dir");
private OWLAPIAlignment alignment = null;
private Ontology onto1 = null;
private Ontology onto2 = null;
@BeforeClass(groups = { "full", "noling" })
private void init(){
alignment = new OWLAPIAlignment();
}
@Test(groups = { "full", "noling" })
public void loadingAndConvertingTest() throws Exception {
assertNotNull( alignment, "Alignment was null" );
AlignmentParser aparser = new AlignmentParser( 0 );
assertNotNull( aparser, "AlignmentParser was null" );
URIAlignment result = (URIAlignment)aparser.parse( "file:examples/rdf/newsample.rdf" );
assertNotNull( result, "URIAlignment(result) was null" );
alignment = OWLAPIAlignment.toOWLAPIAlignment( result );
assertNotNull( alignment, "toOWLAPIAlignment(result) was null" );
result = alignment.toURIAlignment();
assertNotNull( result, "toURIAlignment() was null" );
assertTrue( result instanceof URIAlignment );
}
@Test(groups = { "full", "noling" }, dependsOnMethods = {"loadingAndConvertingTest"})
public void basicAttributeTest() throws Exception {
assertEquals( alignment.getLevel(), "0" );
assertEquals( alignment.getType(), "**" );
assertEquals( alignment.getExtension( Annotations.ALIGNNS, Annotations.METHOD), "fr.inrialpes.exmo.align.impl.method.StringDistAlignment" );
assertEquals( alignment.getExtension( Annotations.ALIGNNS, Annotations.TIME), "7" );
}
@Test(groups = { "full", "noling" }, dependsOnMethods = {"loadingAndConvertingTest"})
public void ontologyTest() throws Exception {
onto1 = alignment.getOntologyObject1();
onto2 = alignment.getOntologyObject2();
assertTrue( onto1 instanceof LoadedOntology );
assertTrue( onto2 instanceof LoadedOntology );
assertTrue( alignment.getOntology1() instanceof OWLOntology );
assertTrue( alignment.getOntology2() instanceof OWLOntology );
assertEquals( alignment.getOntology1URI().toString(), "http://www.example.org/ontology1" );
assertEquals( alignment.getOntology2URI().toString(), "http://www.example.org/ontology2" );
assertEquals( onto1.getURI().toString(), "http://www.example.org/ontology1" );
assertEquals( onto2.getURI().toString(), "http://www.example.org/ontology2" );
assertEquals( onto1.getFile().toString(), "file:examples/rdf/onto1.owl" );
assertEquals( onto2.getFile().toString(), "file:examples/rdf/onto2.owl" );
assertEquals( onto1.getFormalism(), "OWL1.0" );
assertEquals( onto2.getFormalism(), "OWL1.0" );
assertEquals( onto1.getFormURI().toString(), "http://www.w3.org/2002/07/owl#" );
assertEquals( onto2.getFormURI().toString(), "http://www.w3.org/2002/07/owl#" );
}
@Test(groups = { "full", "noling" }, dependsOnMethods = {"ontologyTest"})
public void basicCellTest() throws Exception {
assertEquals( alignment.nbCells(), 2 );
Object ob2 = ((LoadedOntology)onto2).getEntity( new URI("http://www.example.org/ontology2#journalarticle") );
assertTrue( ob2 instanceof OWLEntity );
Set<Cell> s2 = alignment.getAlignCells2( ob2 );
assertEquals( s2.size(), 2 );
for( Cell c2 : s2 ){
assertTrue( c2 instanceof OWLAPICell );
assertTrue( c2.getRelation() instanceof EquivRelation );
assertTrue( c2.getObject1() instanceof OWLEntity );
}
Object ob1 = ((LoadedOntology)onto1).getEntity( new URI("http://www.example.org/ontology1#journalarticle") );
assertTrue( ob1 instanceof OWLEntity );
Set<Cell> s1 = alignment.getAlignCells1( ob1 );
assertEquals( s1.size(), 1 );
for( Cell c1 : s1 ){
assertTrue( c1 instanceof OWLAPICell );
assertTrue( c1.getRelation() instanceof EquivRelation );
assertEquals( c1.getStrength(), 1. );
assertTrue( c1.getObject2() instanceof OWLEntity );
assertEquals( ((LoadedOntology)onto2).getEntityURI( c1.getObject2() ).toString(), "http://www.example.org/ontology2#journalarticle" );
}
ob1 = ((LoadedOntology)onto1).getEntity( new URI("http://www.example.org/ontology1#reviewedarticle") );
assertTrue( ob1 instanceof OWLEntity );
s1 = alignment.getAlignCells1( ob1 );
assertEquals( s1.size(), 1 );
for( Cell c1 : s1 ){
assertTrue( c1 instanceof OWLAPICell );
assertTrue( c1.getRelation() instanceof EquivRelation );
assertEquals( c1.getStrength(), .4666666666666667 );
assertTrue( c1.getObject2() instanceof OWLEntity );
assertEquals( ((LoadedOntology)onto2).getEntityURI( c1.getObject2() ).toString(), "http://www.example.org/ontology2#journalarticle" );
}
}
@Test(groups = { "full", "noling" }, dependsOnMethods = {"loadingAndConvertingTest"})
public void rendererTest() throws Exception {
ByteArrayOutputStream stream = new ByteArrayOutputStream();
//FileOutputStream stream = new FileOutputStream("result.rdf");
PrintWriter writer = new PrintWriter (
new BufferedWriter(
new OutputStreamWriter( stream, "UTF-8" )), true);
AlignmentVisitor renderer = new RDFRendererVisitor( writer );
alignment.render( renderer );
writer.flush();
writer.close();
assertEquals( stream.toString().length(), 1706, "Rendered differently" );
}
}
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